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Estimated time of infection vs. confirmed infections

Following the ideas from Tomas Pueyo's Medium post "Coronavirus: Why You Must Act Now" [1], we assume the average time from infection to death at 23 days [2]. The data is pulled from the COVID-19 Data Repository by Johns Hopkins CSSE [3] every hour. Countries with a minimnum of 1000 confirmed cases and 40 confirmed deaths are included in this analysis.

The time from infection to death is equal to the incubation period plus the time from symptoms to death. This is used to estimate the time of the infections that lead to the observed deaths. We take the last fatality rate per country (total_cases/total_deaths) to estimate the number of infections that are responsible for the observed deaths.

In the figures below, you can observe successive waves of infections (dashed), detections (black) and deaths (red) for each country. The upper panel shows the absolute number of events. The dashed lines show the estimated number of infections. The lower panel shows the normalized number of events. Here the temporal delay between the waves and the relative change between each other can be observed.

[1] https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

[2] https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus

[3] https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

US
Brazil
India
Mexico
Peru
Russia
Indonesia
United Kingdom
Italy
Colombia
Iran
France
Argentina
Germany
South Africa
Spain
Poland
Turkey
Ukraine
Chile
Philippines
Romania
Ecuador
Czechia
Hungary
Canada
Pakistan
Bangladesh
Belgium
Tunisia
Malaysia
Iraq
Bulgaria
Bolivia
Netherlands
Portugal
Japan
Burma
Egypt
Vietnam
Paraguay
Thailand
Kazakhstan
Sweden
Greece
Morocco
Guatemala
Slovakia
Sri Lanka
Nepal
Switzerland
Austria
Jordan
Bosnia and Herzegovina
Honduras
Saudi Arabia
Georgia
Croatia
Lebanon
Serbia
Israel
Afghanistan
Panama
Cuba
Moldova
North Macedonia
Azerbaijan
Uruguay
Costa Rica
Algeria
Ireland
Armenia
Ethiopia
Kenya
Lithuania
China
Zimbabwe
Slovenia
Libya
Venezuela
Oman
Dominican Republic
Belarus
West Bank and Gaza
Zambia
Namibia
Uganda
El Salvador
Kosovo
Sudan
Nigeria
Latvia
Denmark
Kyrgyzstan
Albania
Kuwait
South Korea
Botswana
Malawi
Syria
Cambodia
United Arab Emirates
Mozambique
Senegal
Montenegro
Jamaica
Trinidad and Tobago
Bahrain
Angola
Cameroon
Estonia
Rwanda
Eswatini
Uzbekistan
Australia
Ghana
Mongolia
Congo (Kinshasa)
Somalia
Finland
Madagascar
Norway
Taiwan*
Luxembourg
Suriname
Mauritania
Guyana
Qatar
Haiti
Fiji
Cote d'Ivoire
Mali
Cyprus
Bahamas
Malta
Lesotho
Belize
Guinea
Cabo Verde
Maldives
Hong Kong
Togo
Papua New Guinea
Nicaragua
Congo (Brazzaville)
Gabon
Burkina Faso
Djibouti
Saint Lucia
Benin
Equatorial Guinea
Andorra
Tajikistan
South Sudan
Seychelles
Timor-Leste
Central African Republic

Ahead of the curve

Some countries start testing the population earlier in the outbreak than others. The time delay between the wave of deaths and the wave of confirmed cases is indicative for how early a country is detecting new cases ahead of the increase of deaths. Earlier detection means a better chances for successful isolation of an infected person and treatment of the desease.

We measure the distance of the maximum of cumulative deaths and new deaths to the number of infections to estimate the progression of the infection across countries.

If, in the early phase of the infection wave, the number of deaths rises faster than the number of confirmed cases, the distance drops, indicating that

A comparison of countries with respect to their mean time for reponse is presented below.

To determine the above values, we plot the number of confirmed cases (solid black lines) and the number of deaths (dashed black lines). From this, we measure the distance of the day of maximum deaths (dashed red lines) to the day of confirmed cases at this y-value.

The distance is indicative for how fast the humber of confirmed cases increases comapred to the increase of the number of deaths.

US
Brazil
India
Mexico
Peru
Russia
Indonesia
United Kingdom
Italy
Colombia
Iran
France
Argentina
Germany
South Africa
Spain
Poland
Turkey
Ukraine
Chile
Philippines
Romania
Ecuador
Czechia
Hungary
Canada
Pakistan
Bangladesh
Belgium
Tunisia
Malaysia
Iraq
Bulgaria
Bolivia
Netherlands
Portugal
Japan
Burma
Egypt
Vietnam
Paraguay
Thailand
Kazakhstan
Sweden
Greece
Morocco
Guatemala
Slovakia
Sri Lanka
Nepal
Switzerland
Austria
Jordan
Bosnia and Herzegovina
Honduras
Saudi Arabia
Georgia
Croatia
Lebanon
Serbia
Israel
Afghanistan
Panama
Cuba
Moldova
North Macedonia
Azerbaijan
Uruguay
Costa Rica
Algeria
Ireland
Armenia
Ethiopia
Kenya
Lithuania
China
Zimbabwe
Slovenia
Libya
Venezuela
Oman
Dominican Republic
Belarus
West Bank and Gaza
Zambia
Namibia
Uganda
El Salvador
Kosovo
Sudan
Nigeria
Latvia
Denmark
Kyrgyzstan
Albania
Kuwait
South Korea
Botswana
Malawi
Syria
Cambodia
United Arab Emirates
Mozambique
Senegal
Montenegro
Jamaica
Trinidad and Tobago
Bahrain
Angola
Cameroon
Estonia
Rwanda
Eswatini
Uzbekistan
Australia
Ghana
Mongolia
Congo (Kinshasa)
Somalia
Finland
Madagascar
Norway
Taiwan*
Luxembourg
Suriname
Mauritania
Guyana
Qatar
Haiti
Fiji
Cote d'Ivoire
Mali
Cyprus
Bahamas
Malta
Lesotho
Belize
Guinea
Cabo Verde
Maldives
Hong Kong
Togo
Papua New Guinea
Nicaragua
Congo (Brazzaville)
Gabon
Burkina Faso
Djibouti
Saint Lucia
Benin
Equatorial Guinea
Andorra
Tajikistan
South Sudan
Seychelles
Timor-Leste
Central African Republic